Merge branch 'ongoing-scan-data-warning' into 'v3'

Stop reading scan_data.json for ongoing scan.

Closes #583

See merge request openflexure/openflexure-microscope-server!426

src/openflexure_microscope_server/scan_directories.py

@@ -276,11 +276,15 @@ class ScanDirectoryManager:
         return [f.name for f in os.scandir(self._base_scan_dir) if f.is_dir()]
 
     @requires_lock
-    def all_scans_info(self) -> list[ScanInfo]:
+    def all_scans_info(self, ongoing: Optional[str] = None) -> list[ScanInfo]:
         """Return a lists of ScanInfo objects for each scan."""
         all_info: list[ScanInfo] = []
         for scan_name in self.all_scans:
-            all_info.append(ScanDirectory(scan_name, self.base_dir).scan_info())
+            # If the scan is ongoing send flag to skip reading the json data
+            skip_json = scan_name == ongoing
+            scan_dir = ScanDirectory(scan_name, self.base_dir)
+            info = scan_dir.scan_info(skip_json=skip_json)
+            all_info.append(info)
         return all_info
 
     @requires_lock
@@ -504,7 +508,7 @@ class ScanDirectory:
             LOGGER.warning(f"Could not validate scan data for {self.name}.")
             return None
 
-    def scan_info(self) -> ScanInfo:
+    def scan_info(self, skip_json: bool = False) -> ScanInfo:
         """Return the information to be used in the UI for the scan."""
         scan_files = self.get_scan_files()
         scan_images = self._extract_scan_images(scan_files)
@@ -514,7 +518,7 @@ class ScanDirectory:
         stitch_available = len(stitches) > 0
         dzi = None if not dzi_files else str(dzi_files[0])
 
-        scan_data = self.get_scan_data()
+        scan_data = None if skip_json else self.get_scan_data()
         duration = (
             None
             if scan_data is None or scan_data.duration is None

src/openflexure_microscope_server/things/smart_scan.py

@@ -49,8 +49,8 @@ CSMDep = lt.deps.direct_thing_client_dependency(
 AutofocusDep = lt.deps.direct_thing_client_dependency(AutofocusThing, "/autofocus/")
 
 
-class ScanListData(BaseModel):
+class ScanListInfo(BaseModel):
-    """The data to be sent to the Scan List tab."""
+    """The information to be sent to the Scan List tab."""
 
     scans: list[scan_directories.ScanInfo]
     """The list of scans as ScanInfo objects"""
@@ -588,8 +588,18 @@ class SmartScanThing(lt.Thing):
     )
     """Whether to run a final stitch at the end of a successful scan."""
 
+    def _get_all_scan_info(self) -> list[scan_directories.ScanInfo]:
+        """Return all the information from the scan directories.
+
+        It is preferable to use the method rather than calling
+        _scan_dir_manager.all_scans_info() directly as it will handle stopping the json
+        in any ongoing scans being read.
+        """
+        ongoing_name = None if self._ongoing_scan is None else self._ongoing_scan.name
+        return self._scan_dir_manager.all_scans_info(ongoing=ongoing_name)
+
     @lt.thing_property
-    def scans(self) -> ScanListData:
+    def scans(self) -> ScanListInfo:
         """All the available scans.
 
         Each scan has a name (which can be used to access it), along with
@@ -598,8 +608,8 @@ class SmartScanThing(lt.Thing):
         uses a regular expression, and changes to the naming scheme will
         break it.
         """
-        return ScanListData(
+        return ScanListInfo(
-            scans=self._scan_dir_manager.all_scans_info(),
+            scans=self._get_all_scan_info(),
             ongoing=None if self._ongoing_scan is None else self._ongoing_scan.name,
         )
 
@@ -667,7 +677,7 @@ class SmartScanThing(lt.Thing):
     def purge_empty_scans(self, logger: lt.deps.InvocationLogger) -> None:
         """Delete all scan folders containing no images at the top level."""
         # JSON is ignored as it's created before any images are captured
-        for scan_info in self._scan_dir_manager.all_scans_info():
+        for scan_info in self._get_all_scan_info():
             if scan_info.number_of_images == 0:
                 self._delete_scan(scan_info.name, logger)
 
@@ -791,6 +801,6 @@ class SmartScanThing(lt.Thing):
         """
         if self._scan_logger is not None:
             raise RuntimeError("Can't stitch previous scans while a scan is ongoing")
-        for scan in self._scan_dir_manager.all_scans_info():
+        for scan in self._get_all_scan_info():
             if scan.dzi is None:
                 self.stitch_scan(logger=logger, cancel=cancel, scan_name=scan.name)

tests/test_scan_directories.py

@@ -170,15 +170,23 @@ def test_bad_scan_names():
     assert scan_dir.name == "fake_scan_rm_-rf____0001"
 
 
-def test_scan_sequence_and_listing():
+def test_scan_sequence_and_listing(caplog):
     """Check created scans are added in order and listed correctly."""
     _clear_scan_dir()
     scan_dir_manager = ScanDirectoryManager(BASE_SCAN_DIR)
+
+    # Create some scan data and mark it as successful to get an end date.
+    scan_data = _fake_scan_data()
+    scan_data.set_final_data(result="Success")
     # Make 4 scans
-    scan_dir_manager.new_scan_dir("fake_scan")
+    scan_dir = scan_dir_manager.new_scan_dir("fake_scan")
-    scan_dir_manager.new_scan_dir("fake_scan")
+    scan_dir.save_scan_data(scan_data)
-    scan_dir_manager.new_scan_dir("fake_scan")
+    scan_dir = scan_dir_manager.new_scan_dir("fake_scan")
-    scan_dir_manager.new_scan_dir("fake_scan")
+    scan_dir.save_scan_data(scan_data)
+    scan_dir = scan_dir_manager.new_scan_dir("fake_scan")
+    scan_dir.save_scan_data(scan_data)
+    scan_dir = scan_dir_manager.new_scan_dir("fake_scan")
+    scan_dir.save_scan_data(scan_data)
 
     # Check they exist and are numbered sequentially
     all_scans = scan_dir_manager.all_scans
@@ -188,13 +196,55 @@ def test_scan_sequence_and_listing():
     assert "fake_scan_0003" in all_scans
     assert "fake_scan_0004" in all_scans
 
-    # Check scan data can be read for all of them
+    # Start capturing warnings
-    # (more detailed scan_info tests below)
+    with caplog.at_level(logging.WARNING):
-    all_scan_info = scan_dir_manager.all_scans_info()
+        # Check scan data can be read for all of them
-    for scan_info in all_scan_info:
+        # (more detailed scan_info tests below)
-        assert isinstance(scan_info, ScanInfo)
+        all_scan_info = scan_dir_manager.all_scans_info()
-        assert scan_info.name.startswith("fake_scan_000")
+        for scan_info in all_scan_info:
-        assert scan_info.number_of_images == 0
+            assert isinstance(scan_info, ScanInfo)
+            assert scan_info.name.startswith("fake_scan_000")
+            assert scan_info.number_of_images == 0
+            assert scan_info.duration is not None
+        # There are no warnings or errors
+        assert len(caplog.records) == 0
+
+        # Mess up the JSON of the final scan
+        with open(scan_dir.scan_data_path, "w", encoding="utf-8") as f:
+            f.write("Mock JSON")
+
+        # Re-read the data with bad data for fake_scan_0004
+        all_scan_info = scan_dir_manager.all_scans_info()
+        for scan_info in all_scan_info:
+            assert isinstance(scan_info, ScanInfo)
+            assert scan_info.name.startswith("fake_scan_000")
+            assert scan_info.number_of_images == 0
+            # Bad data for scan 0004. So duration is None.
+            if scan_info.name == "fake_scan_0004":
+                assert scan_info.duration is None
+            else:
+                assert scan_info.duration is not None
+        # This should have warned about the bad data
+        assert len(caplog.records) == 1
+        assert (
+            caplog.records[0].message == "Could not load scan data for fake_scan_0004."
+        )
+
+        # Clear the warning logs
+        caplog.clear()
+        # Re-read the data again claiming fake_scan_0004 is ongoing
+        all_scan_info = scan_dir_manager.all_scans_info(ongoing="fake_scan_0004")
+        for scan_info in all_scan_info:
+            assert isinstance(scan_info, ScanInfo)
+            assert scan_info.name.startswith("fake_scan_000")
+            assert scan_info.number_of_images == 0
+            # scan 0004 is marked as ongoing, so duration is None.
+            if scan_info.name == "fake_scan_0004":
+                assert scan_info.duration is None
+            else:
+                assert scan_info.duration is not None
+        # This time there is no warning
+        assert len(caplog.records) == 0
 
 
 def test_scan_name_non_sequential():

webapp/src/components/tabContentComponents/scanListComponents/scanCard.vue

@@ -58,8 +58,9 @@
       <div class="scan-info">
         <ul>
           <li>{{ scanData.number_of_images }} images</li>
-          <li>created: {{ formatDate(scanData.created) }}</li>
+          <li>Created: {{ formatDate(scanData.created) }}</li>
-          <li>duration: {{ formatDuration(scanData.duration) }}</li>
+          <li v-if="!ongoing">Duration: {{ formatDuration(scanData.duration) }}</li>
+          <li v-if="ongoing">Duration: <i>Ongoing</i></li>
         </ul>
         <ul v-if="!ongoing">
           <li v-if="scanData.number_of_images < 3" class="warning-msg">